Alignments for a candidate for fadA in Dechlorosoma suillum PS

GapMind for catabolism of small carbon sources

Alignments for a candidate for fadA in Dechlorosoma suillum PS

Align Beta-ketothiolase BktB; Acetyl-CoA acetyltransferase; Acetyl-CoA acyltransferase; EC 2.3.1.16; EC 2.3.1.9 (characterized)
to candidate Dsui_3239 Dsui_3239 acetyl-CoA acetyltransferase

Query= SwissProt::Q0KBP1
         (394 letters)



>FitnessBrowser__PS:Dsui_3239
          Length = 392

 Score =  429 bits (1104), Expect = e-125
 Identities = 219/394 (55%), Positives = 285/394 (72%), Gaps = 2/394 (0%)

Query: 1   MTREVVVVSGVRTAIGTFGGSLKDVAPAELGALVVREALARAQVSGDDVGHVVFGNVIQT 60
           M++E+VV+S VR+A+G FGGSL  + PAELG LVV+EA+ARA V    V     GN I T
Sbjct: 1   MSKEIVVLSAVRSAVGGFGGSLAGMEPAELGGLVVKEAIARAGVDPKAVTFATVGNCIPT 60

Query: 61  EPRDMYLGRVAAVNGGVTINAPALTVNRLCGSGLQAIVSAAQTILLGDTDVAIGGGAESM 120
           E R  Y+ R+A + GG+++++ A  VNRLCGS +QAIVS+AQ I+LGD D AIGGG E M
Sbjct: 61  ETRYAYVARLATIQGGMSMDSVAFAVNRLCGSAMQAIVSSAQAIMLGDADYAIGGGVEVM 120

Query: 121 SRAPYLAPAARWGARMGDAGLVDMMLGALHDPFHRIHMGVTAENVAKEYDISRAQQDEAA 180
           SR  YL PA R GARMGD   +D M+  L DPF   HMG+TAEN+  ++ ++R +QD  A
Sbjct: 121 SRGAYLLPALRSGARMGDTKAIDAMVSVLTDPFGVGHMGITAENLVTKWGLTREEQDAFA 180

Query: 181 LESHRRASAAIKAGYFKDQIVPVVSKGRKGDVTFDTDEHVRHDATIDDMTKLRPVFVKEN 240
           LES  RA+ AI  G FK QIVP+  + +KGDV FDTDEH R   T++ + K++  F K++
Sbjct: 181 LESQNRAAKAIAEGRFKSQIVPITFQTKKGDVVFDTDEHPR-ATTMEALAKMKAAF-KKD 238

Query: 241 GTVTAGNASGLNDAAAAVVMMERAEAERRGLKPLARLVSYGHAGVDPKAMGIGPVPATKI 300
           G+VTAGNASG+NDAAA +V+ + A+A   G KP+ARLVSY  AGV  + MG GP+P++K+
Sbjct: 239 GSVTAGNASGINDAAAFLVLADAAKAAAAGHKPIARLVSYAIAGVPNEIMGEGPIPSSKL 298

Query: 301 ALERAGLQVSDLDVIEANEAFAAQACAVTKALGLDPAKVNPNGSGISLGHPIGATGALIT 360
           AL++AGL +  +D++E+NEAFAAQ+ AV K LGLDPAK N NG  I+LGHP+GATG +I 
Sbjct: 299 ALQKAGLTLDQIDLVESNEAFAAQSLAVAKGLGLDPAKTNVNGGAIALGHPVGATGGVIV 358

Query: 361 VKALHELNRVQGRYALVTMCIGGGQGIAAIFERI 394
            K LHE+ R   RY + TMCIGGGQGI  I+ERI
Sbjct: 359 TKLLHEMQRTGARYGMATMCIGGGQGITTIYERI 392


Lambda     K      H
   0.318    0.134    0.381 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 440
Number of extensions: 14
Number of successful extensions: 2
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 394
Length of database: 392
Length adjustment: 31
Effective length of query: 363
Effective length of database: 361
Effective search space:   131043
Effective search space used:   131043
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 50 (23.9 bits)

Align candidate Dsui_3239 Dsui_3239 (acetyl-CoA acetyltransferase)
to HMM TIGR01930 (acetyl-CoA C-acyltransferase (EC 2.3.1.16))

# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  ../tmp/path.carbon/TIGR01930.hmm
# target sequence database:        /tmp/gapView.802.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01930  [M=385]
Accession:   TIGR01930
Description: AcCoA-C-Actrans: acetyl-CoA C-acyltransferase
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   6.6e-129  416.1  12.0   7.6e-129  415.9  12.0    1.0  1  lcl|FitnessBrowser__PS:Dsui_3239  Dsui_3239 acetyl-CoA acetyltrans


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__PS:Dsui_3239  Dsui_3239 acetyl-CoA acetyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  415.9  12.0  7.6e-129  7.6e-129       1     385 []       7     390 ..       7     390 .. 0.98

  Alignments for each domain:
  == domain 1  score: 415.9 bits;  conditional E-value: 7.6e-129
                         TIGR01930   1 ivdavRtpigklggslkelsaedLlaavikelleragldpekidevilGnvlqageq.aniaReaalaaglpesvpa 76 
                                       +++avR+++g +ggsl+ +++++L+  v+ke+++rag+dp+++  + +Gn +++ +  a +aR a+++ g++ +  a
  lcl|FitnessBrowser__PS:Dsui_3239   7 VLSAVRSAVGGFGGSLAGMEPAELGGLVVKEAIARAGVDPKAVTFATVGNCIPTETRyAYVARLATIQGGMSMDSVA 83 
                                       689*******99*********************************************9******************* PP

                         TIGR01930  77 ltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgkakledqllkdl..vktklsm 151
                                       ++vnr+C+S++qA+ + aq+i+ G+ad ++ GGvE mSr  +ll+a   r+++++g++k  d++++ l  +    +m
  lcl|FitnessBrowser__PS:Dsui_3239  84 FAVNRLCGSAMQAIVSSAQAIMLGDADYAIGGGVEVMSRGAYLLPAL--RSGARMGDTKAIDAMVSVLtdPFGVGHM 158
                                       *********************************************97..89***********9999999988999** PP

                         TIGR01930 152 getAenlakkygisReeqDeyalrShqkaakAieegkfkdeivpvevkgk..kkvvskDegirpnttlekLakLkpa 226
                                       g+tAenl +k+g++ReeqD++al+S+++aakAi+eg+fk++ivp+++++k  ++v+++De++r  tt+e+Lak+k+a
  lcl|FitnessBrowser__PS:Dsui_3239 159 GITAENLVTKWGLTREEQDAFALESQNRAAKAIAEGRFKSQIVPITFQTKkgDVVFDTDEHPR-ATTMEALAKMKAA 234
                                       ************************************************99999**********.899********** PP

                         TIGR01930 227 fkekkgstvtAgNssqlnDGAaalllmseevakelgltplarivsaavagvdpeemglgpvpAiekaLkkaglsisd 303
                                       fk+ +gs vtAgN+s++nD+Aa+l+l+  ++a++ g +p+ar+vs+a+agv+ e+mg gp+p+++ aL+kagl++++
  lcl|FitnessBrowser__PS:Dsui_3239 235 FKK-DGS-VTAGNASGINDAAAFLVLADAAKAAAAGHKPIARLVSYAIAGVPNEIMGEGPIPSSKLALQKAGLTLDQ 309
                                       *95.9*7.********************************************************************* PP

                         TIGR01930 304 idlvEinEAFAaqvlavekelgsldlekvNvnGGAiAlGHPlGasGarivltllkeLkergkkyGlatlCvggGqGa 380
                                       idlvE nEAFAaq lav+k lg ld++k NvnGGAiAlGHP+Ga+G+ iv++ll+e+++ g++yG+at+C+ggGqG+
  lcl|FitnessBrowser__PS:Dsui_3239 310 IDLVESNEAFAAQSLAVAKGLG-LDPAKTNVNGGAIALGHPVGATGGVIVTKLLHEMQRTGARYGMATMCIGGGQGI 385
                                       **********************.99**************************************************** PP

                         TIGR01930 381 Avile 385
                                       ++i e
  lcl|FitnessBrowser__PS:Dsui_3239 386 TTIYE 390
                                       99975 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (385 nodes)
Target sequences:                          1  (392 residues searched)
Passed MSV filter:                         1  (1); expected 0.0 (0.02)
Passed bias filter:                        1  (1); expected 0.0 (0.02)
Passed Vit filter:                         1  (1); expected 0.0 (0.001)
Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
Initial search space (Z):                  1  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 8.64
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory

GapMind for catabolism of small carbon sources